Air accident investigators began work Sunday to establish the cause of a crash that saw two passengers killed and scores injured as a Boeing 777 burst into flames on landing at San Francisco International Airport.

Asiana Airlines Flight 214 from Seoul appeared to lose control after touching down on Saturday, losing its tail and spreading debris along the runway before coming to a rest in flames.

Nearly all of the 307 passengers and crew members on board were able to make it out alive, but many remained in hospital Sunday, being treated for injuries that ranged from bruises and cuts to more serious conditions.

Authorities confirmed that two bodies had been retrieved from outside of the plane's wreckage. The deceased were later named as Ye Mengyuan and Wang Linjia, two 16-year-old girls from China's eastern Zhejiang province.

Meanwhile, investigators began the task of trying to establish what caused the incident.

The head of Asiana Airlines appeared to rule out mechanical failure as a cause.

"For now, we acknowledge that there were no problems caused by the 777-200 plane or [its] engines," Yoon Young-doo told a press conference on Sunday.

But airline representatives would not be drawn on whether they believed pilot error or a mistake from the airport's control tower could be to blame.

Investigators hope that the airplane's black box may yield more clues. The flight data recorder was taken overnight to Washington, DC, where it will be further examined, officials said. They also plan to interview the pilots, the crew and passengers.

Speaking on NBC's Meet the Press, Deborah Hersman, head of the National Transportation Safety Board (NTSB), said her team were looking into the role that the shutdown of a key navigational aid may have played in the crash. She said the glide slope – a ground-based aid that helps pilots stay on course while landing – had not been used since June.

She added that pilots had been sent a notice warning that the device was no longer available and that there were many other navigation tools available to help pilots land. She says investigators will be "taking a look at it all."

Meanwhile, witness accounts of the plane's approach have led some to question if the craft may have been coming in too low, catching part of a small seawall at the foot of the runway.

San Francisco is one of several airports around the country that border bodies of water that have walls at the end of their runways to prevent planes that overrun a runway from ending up in the water.

Noting the extent of the damage to the aircraft, Hersman said she was "thankful" that the death toll was not higher.

The two fatalities were passengers seated at the rear of the plane, an area that received extensive damage during the crash landing. Their bodies were found "exterior" to the wreckage, according to San Francisco fire department chief Joanne Hayes-White.

"Having surveyed that area, we're lucky that there hasn't been a greater loss," she added.

During the plane's evacuation, police officers threw utility knives up to crew members inside the burning wreckage so they could cut away passengers' seat belts. Passengers jumped down emergency slides, escaping the smoke. One walked through a hole where a rear bathroom had been.

"It's miraculous we survived," said passenger Vedpal Singh, who had a fractured collarbone and whose arm was in a sling.

Hayes-White said 19 people remain hospitalised on Sunday, six of them in critical condition.

She said at a news conference outside San Francisco General Hospital the two 16-year-old girls who died were found on either side of the plane near the "front middle". Investigators are determining whether they were alive or dead when rescuers reached the scene.

Hayes-White said first responders told her they saw people at the edge of the bay dousing themselves with water, possibly to cool burn injuries.

The plane carried 141 Chinese passengers, 77 South Koreans, 61 Americans, three Canadians, three from India, one Japanese, one Vietnamese and one from France, while the nationalities of the remaining three haven't been confirmed.

Four pilots were aboard the plane, and they rotated on a two-person shift during the flight, according to the Ministry of Land, Infrastructure and Transport in South Korea. The two who piloted the plane at the time of crash were Lee Jeong-min and Lee Gang-guk.

Yoon, the Asiana president, described the pilots as "skilled", saying three had logged more than 10,000 hours each of flight time. He said the fourth had put in almost that much time, but officials later corrected that to say the fourth had logged nearly 5,000 hours. All four are South Korean.

During a televised news conference, Yoon bowed his head and expressed his personal regert over the incident.

"I am bowing my head and extending my deep apology" to the passengers, their families and the South Korean people over the crash, he said.